ECB-ART-40009
Science
2006 Nov 10;3145801:941-52. doi: 10.1126/science.1133609.
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The genome of the sea urchin Strongylocentrotus purpuratus.
Sea Urchin Genome Sequencing Consortium
,
Sodergren E
,
Weinstock GM
,
Davidson EH
,
Cameron RA
,
Gibbs RA
,
Angerer RC
,
Angerer LM
,
Arnone MI
,
Burgess DR
,
Burke RD
,
Coffman JA
,
Dean M
,
Elphick MR
,
Ettensohn CA
,
Foltz KR
,
Hamdoun A
,
Hynes RO
,
Klein WH
,
Marzluff W
,
McClay DR
,
Morris RL
,
Mushegian A
,
Rast JP
,
Smith LC
,
Thorndyke MC
,
Vacquier VD
,
Wessel GM
,
Wray G
,
Zhang L
,
Elsik CG
,
Ermolaeva O
,
Hlavina W
,
Hofmann G
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Kitts P
,
Landrum MJ
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Mackey AJ
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Maglott D
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Panopoulou G
,
Poustka AJ
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Pruitt K
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Sapojnikov V
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Song X
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Souvorov A
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Solovyev V
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Wei Z
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Whittaker CA
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Worley K
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Durbin KJ
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Shen Y
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Fedrigo O
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Garfield D
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Haygood R
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Primus A
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Satija R
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Severson T
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Gonzalez-Garay ML
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Jackson AR
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Milosavljevic A
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Tong M
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Killian CE
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Livingston BT
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Wilt FH
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Adams N
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Bellé R
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Carbonneau S
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Cheung R
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Cormier P
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Cosson B
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Croce J
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Croce J
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Fernandez-Guerra A
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Genevière AM
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Goel M
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Kelkar H
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Morales J
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Mulner-Lorillon O
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Robertson AJ
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Goldstone JV
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Cole B
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Epel D
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Gold B
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Hahn ME
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Howard-Ashby M
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Scally M
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Stegeman JJ
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Allgood EL
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Cool J
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Judkins KM
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McCafferty SS
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Musante AM
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Obar RA
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Rawson AP
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Rossetti BJ
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Gibbons IR
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Hoffman MP
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Leone A
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Istrail S
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Materna SC
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Samanta MP
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Stolc V
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Tongprasit W
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Tu Q
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Bergeron KF
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Brandhorst BP
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Whittle J
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Berney K
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Bottjer DJ
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Calestani C
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Peterson K
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Chow E
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Yuan QA
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Elhaik E
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Graur D
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Reese JT
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Bosdet I
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Heesun S
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Marra MA
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Schein J
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Anderson MK
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Brockton V
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Buckley KM
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Cohen AH
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Fugmann SD
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Hibino T
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Loza-Coll M
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Majeske AJ
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Messier C
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Nair SV
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Pancer Z
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Terwilliger DP
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Agca C
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Arboleda E
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Chen N
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Churcher AM
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Hallböök F
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Humphrey GW
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Idris MM
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Kiyama T
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Liang S
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Mellott D
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Mu X
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Murray G
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Olinski RP
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Raible F
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Rowe M
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Taylor JS
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Tessmar-Raible K
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Wang D
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Wilson KH
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Yaguchi S
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Gaasterland T
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Galindo BE
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Gunaratne HJ
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Juliano C
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Kinukawa M
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Moy GW
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Neill AT
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Nomura M
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Raisch M
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Reade A
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Roux MM
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Song JL
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Su YH
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Townley IK
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Voronina E
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Wong JL
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Amore G
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Branno M
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Brown ER
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Cavalieri V
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Duboc V
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Duloquin L
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Flytzanis C
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Gache C
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Lapraz F
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Lepage T
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Locascio A
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Martinez P
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Matassi G
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Matranga V
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Range R
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Rizzo F
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Röttinger E
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Beane W
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Bradham C
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Byrum C
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Glenn T
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Hussain S
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Manning G
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Miranda E
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Thomason R
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Walton K
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Wikramanayke A
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Wu SY
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Xu R
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Brown CT
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Chen L
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Gray RF
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Lee PY
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Nam J
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Oliveri P
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Smith J
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Muzny D
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Bell S
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Chacko J
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Cree A
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Curry S
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Davis C
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Dinh H
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Dugan-Rocha S
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Fowler J
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Gill R
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Hamilton C
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Hernandez J
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Hines S
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Hume J
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Jackson L
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Jolivet A
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Kovar C
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Lee S
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Lewis L
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Miner G
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Morgan M
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Nazareth LV
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Okwuonu G
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Parker D
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Pu LL
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Thorn R
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Wright R
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Abstract
We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
PubMed ID: 17095691
PMC ID: PMC3159423
Article link: Science
Grant support: [+]
P42 ES007381 NIEHS NIH HHS , R37-HD12896 NICHD NIH HHS , GM058231 NIGMS NIH HHS , P01 HD037105 NICHD NIH HHS , 2P42 ESO7381 PHS HHS , F32 HD047136 NICHD NIH HHS , F32 HD047136-03 NICHD NIH HHS , GM61005 NIGMS NIH HHS , R01 ES006272 NIEHS NIH HHS , T32 GM007601 NIGMS NIH HHS , P01 HD039948 NICHD NIH HHS , S19916 Biotechnology and Biological Sciences Research Council , P40 OD010959 NIH HHS , R01 GM061005 NIGMS NIH HHS , P30 CA014051 NCI NIH HHS , R43 CA093106 NCI NIH HHS , R01 GM070840 NIGMS NIH HHS , GM61464 NIGMS NIH HHS , U54 HG003273 NHGRI NIH HHS , P30-CA14051 NCI NIH HHS , F32 ES012794 NIEHS NIH HHS , EY11930 NEI NIH HHS , R01 HD028152 NICHD NIH HHS , R01 EY011930 NEI NIH HHS , F32 ESO12794 PHS HHS , RR-15044 NCRR NIH HHS , R01 HD014483 NICHD NIH HHS , R01 GM058231 NIGMS NIH HHS , HD14483 NICHD NIH HHS , HD039948 NICHD NIH HHS , HD66219 NICHD NIH HHS , F32-HD47136 NICHD NIH HHS , R44 CA093106 NCI NIH HHS , R01ES006272 NIEHS NIH HHS , 5 U54 HG003273 NHGRI NIH HHS , F32 HD047136-02 NICHD NIH HHS , P40 RR015044 NCRR NIH HHS , GM070840 NIGMS NIH HHS , HD-37105 NICHD NIH HHS , R01 ES006272-13 NIEHS NIH HHS , R01 HD066219 NICHD NIH HHS , R01 GM061464 NIGMS NIH HHS , R01 DC020052 NIDCD NIH HHS
Genes referenced: LOC100887844
References [+] :
Akira,
Pathogen recognition and innate immunity.
2006, Pubmed
Akira, Pathogen recognition and innate immunity. 2006, Pubmed
Beane, Lineage-specific expansions provide genomic complexity among sea urchin GTPases. 2006, Pubmed , Echinobase
Britten, The single-copy DNA sequence polymorphism of the sea urchin Strongylocentrotus purpuratus. 1978, Pubmed , Echinobase
Cai, A clone-array pooled shotgun strategy for sequencing large genomes. 2001, Pubmed
Cobb, Anatomical studies of simple invertebrate synapses utilizing stage rotation election microscopy and densitometry. 1977, Pubmed , Echinobase
Davidson, A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. 2002, Pubmed , Echinobase
Davidson, A genomic regulatory network for development. 2002, Pubmed , Echinobase
Dehal, The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. 2002, Pubmed
Dehal, Two rounds of whole genome duplication in the ancestral vertebrate. 2005, Pubmed
Duncan, Control of distal antennal identity and tarsal development in Drosophila by spineless-aristapedia, a homolog of the mammalian dioxin receptor. 1998, Pubmed
Elsik, Creating a honey bee consensus gene set. 2007, Pubmed
Erwin, The last common bilaterian ancestor. 2002, Pubmed
Fugmann, An ancient evolutionary origin of the Rag1/2 gene locus. 2006, Pubmed , Echinobase
Gibbs, Genome sequence of the Brown Norway rat yields insights into mammalian evolution. 2004, Pubmed
Gu, Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. 2002, Pubmed
Hinegardner, An improved fluorometric assay for DNA. 1971, Pubmed
Howard-Ashby, Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus. 2006, Pubmed , Echinobase
Kapitonov, RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. 2005, Pubmed , Echinobase
Kawasaki, Genetic basis for the evolution of vertebrate mineralized tissue. 2004, Pubmed
Koonin, Origin and evolution of eukaryotic apoptosis: the bacterial connection. 2002, Pubmed
Kusserow, Unexpected complexity of the Wnt gene family in a sea anemone. 2005, Pubmed
Manning, Evolution of protein kinase signaling from yeast to man. 2002, Pubmed
Manning, The protein kinase complement of the human genome. 2002, Pubmed
McLysaght, Extensive genomic duplication during early chordate evolution. 2002, Pubmed
Pancer, Dynamic expression of multiple scavenger receptor cysteine-rich genes in coelomocytes of the purple sea urchin. 2000, Pubmed , Echinobase
Pancer, Origins of immunity: transcription factors and homologues of effector genes of the vertebrate immune system expressed in sea urchin coelomocytes. 1999, Pubmed , Echinobase
Qin, The Caenorhabditis elegans aryl hydrocarbon receptor, AHR-1, regulates neuronal development. 2004, Pubmed
Rast, Genomic insights into the immune system of the sea urchin. 2006, Pubmed , Echinobase
Samanta, The transcriptome of the sea urchin embryo. 2006, Pubmed , Echinobase
Smith, The ancestral complement system in sea urchins. 2001, Pubmed , Echinobase
Smith, Complement systems in invertebrates. The ancient alternative and lectin pathways. 1999, Pubmed , Echinobase
Sullivan, StellaBase: the Nematostella vectensis Genomics Database. 2006, Pubmed
Vinson, Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. 2005, Pubmed
Walisser, Aryl hydrocarbon receptor-dependent liver development and hepatotoxicity are mediated by different cell types. 2005, Pubmed
Wei, A database of mRNA expression patterns for the sea urchin embryo. 2006, Pubmed , Echinobase
Xie, Orphan nuclear receptors: the exotics of xenobiotics. 2001, Pubmed